Import MySQL database into a SQL Server

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Use SQL Server Migration Assistant (SSMA)

In addition to MySQL it supports Oracle, Sybase and MS Access.

It appears to be quite smart and capable of handling even nontrivial transfers. It also got some command line interface (in addition to GUI) so theoretically it can be integrated into some batch load process.

This the current download link for MySQL version https://www.microsoft.com/en-us/download/details.aspx?id=54257

The current (June 2016) stable version 6.0.1 crashes with the current (5.3.6) MySQL ODBC driver while transferring data. Everything 64 bit.
The 5.3 version with the 5.1.13 ODBC driver works fine.

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